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Sample GSM788398 Query DataSets for GSM788398
Status Public on Dec 31, 2011
Title RNAi-Root-Control-3
Sample type RNA
 
Source name RNAi_Root_control medium
Organism Arabidopsis halleri
Characteristics genotype: AhNAS2-RNAi-1-2
age: 5 weeks old
tissue: Root
Extracted molecule total RNA
Extraction protocol RNA was extracted from homogenized A. halleri root tissue with Trizol (Invitrogen Life Technologies) according to the manufacturer’s instructions.
Label biotin
Label protocol 250 ng of total RNA, purified with RNeasy Mini columns (Qiagen, Hilden, Germany) according to the manufacturer's directions, were used to generate double-stranded cDNA and subsequently biotin-labeled cRNA. The length of the cRNA products was assessed using an Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, USA)
 
Hybridization protocol cRNA products were hybridized to the array for 16 h at 45C in a rotating chamber.
Scan protocol Hybridized arrays were washed and stained in an Affymetrix Fluidics Station FS450, and the fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000.
Description Hydroponically grown 5-weeks old plants
Data processing CEL files from the Affymetrix microarray hybridization were processed by use of the R program and Bioconductor packages (Gentleman et al., 2004). The Robust Multi-chip Average (RMA) normalization was performed using the default settings of the corresponding R function (Irizarry et al., 2003). To estimate the amount of expressed mRNAs, the present call information of the non-parametric Wilcoxon signed rank test (PMA values) was computed with the 'affy' package (Gautier et al., 2004). Hybridization data from three biological replicates were generated for each Langelsheim wild-type and RNAi line 1-2.
 
Submission date Aug 31, 2011
Last update date Aug 15, 2018
Contact name Stephan Clemens
E-mail(s) stephan.clemens@uni-bayreuth.de
Organization name University of Bayreuth
Department Plant Physiology
Street address Universitaetsstrasse 30
City Bayreuth
ZIP/Postal code 95440
Country Germany
 
Platform ID GPL198
Series (1)
GSE31778 AhNAS2 suppression in Arabidopsis halleri roots
Relations
Reanalyzed by GSE118579

Data table header descriptions
ID_REF
VALUE RMA signal intensity

Data table
ID_REF VALUE
244901_at 6.153324105
244902_at 5.83652023
244903_at 7.214357012
244904_at 5.286958124
244905_at 4.048922737
244906_at 4.646727571
244907_at 3.456544284
244908_at 3.452945041
244909_at 3.691543752
244910_s_at 3.918633272
244911_at 3.027551219
244912_at 8.449834592
244913_at 4.53067724
244914_at 3.23822395
244915_s_at 4.297667057
244916_at 3.863468717
244917_at 3.849293636
244918_at 3.175914556
244919_at 5.820919851
244920_s_at 6.324631462

Total number of rows: 22810

Table truncated, full table size 490 Kbytes.




Supplementary file Size Download File type/resource
GSM788398_A585_18_NAS2_RNA_Ctrl_Exp3.CEL.gz 1.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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